So let's say I am back in the good old days before computers,
hand-calculating the MIR phase of my first reflection--would I just
set that phase to zero, and go from there, i.e. that wave will
define/emanate from the origin?
--------
I do not think this could be done to get the origin correctly defined
(in most cases),
if good old ways were used as did in the good old days. There are many
restrictions on the definition on origins (space group-, actually,
symmetry-dependent), and a simple setting-it-to-0 on phase angle will
cause, or
at least complicates the problem (also see below)-----this could be
imagined from
the reverse way.
And why should I choose f000 over f010
or whatever else? Since I have no access to f000 experimentally, isn't
it strange to define its phase as 0 rather than some other reflection?
--------
The definition is not a simple "setting it to 0". It comes from the
origin of
phases problem. (000) reflection is the sum of the total electrons
(TE) in the
unit cell, based on this physical/crystallographic meaning, the (000)
phase
angle gets to be 0 (otherwise the sum will be less than TE due to at
least one
cos(non-0)). There is no point a shift on this value is applied, but
a counter balance for
this shift will have to be applied during the calculation later if a
shift had been applied.
--------no any merits for this!
Lijun
JPK
On Wed, Oct 13, 2010 at 7:27 PM, Lijun Liu <lijun....@ucsf.edu> wrote:
When talking about the reflection phase:
While we are on embarrassingly simple questions, I have wondered
for a long
time what is the reference phase for reflections? I.e. a given
phase of say
45deg is 45deg relative to what?
=========
Relative to a defined 0.
Is it the centrosymmetric phases?
=====
Yes. It is that of F(000).
Or a theoretical wave from the origin?
=====
No, it is a real one, detectable but not measurable.
Lijun
Jacob Keller
----- Original Message -----
From: "William Scott" <wgsc...@chemistry.ucsc.edu>
To: <CCP4BB@JISCMAIL.AC.UK>
Sent: Wednesday, October 13, 2010 3:58 PM
Subject: [ccp4bb] Summary : [ccp4bb] embarrassingly simple MAD
phasing
question
Thanks for the overwhelming response. I think I probably didn't
phrase the
question quite right, but I pieced together an answer to the
question I
wanted to ask, which hopefully is right.
On Oct 13, 2010, at 1:14 PM, SHEPARD William wrote:
It is very simple, the structure factor for the anomalous scatterer
is
FA = FN + F'A + iF"A (vector addition)
The vector F"A is by definition always +i (90 degrees anti-
clockwise) with
respect to the vector FN (normal scattering), and it represents the
phase
lag in the scattered wave.
So I guess I should have started by saying I knew f'' was
imaginary, the
absorption term, and always needs to be 90 degrees in phase ahead
of the f'
(dispersive component).
So here is what I think the answer to my question is, if I understood
everyone correctly:
Starting with what everyone I guess thought I was asking,
FA = FN + F'A + iF"A (vector addition)
for an absorbing atom at the origin, FN (the standard atomic
scattering
factor component) is purely real, and the f' dispersive term is
purely real,
and the f" absorption term is purely imaginary (and 90 degrees
ahead).
Displacement from the origin rotates the resultant vector FA in the
complex
plane. That implies each component in the vector summation is
rotated by
that same phase angle, since their magnitudes aren't changed from
displacement from the origin, and F" must still be perpendicular to
F'.
Hence the absorption term F" is no longer pointed in the imaginary
axis
direction.
Put slightly differently, the fundamental requirement is that the
positive
90 degree angle between f' and f" must always be maintained, but
their
absolute orientations are only enforced for atoms at the origin.
Please correct me if this is wrong.
Also, since F" then has a projection upon the real axis, it now has
a real
component (and I guess this is also an explanation for why you
don't get
this with centrosymmetric structures).
Thanks again for everyone's help.
-- Bill
William G. Scott
Professor
Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
228 Sinsheimer Laboratories
University of California at Santa Cruz
Santa Cruz, California 95064
USA
phone: +1-831-459-5367 (office)
+1-831-459-5292 (lab)
fax: +1-831-4593139 (fax) =
*******************************************
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
Dallos Laboratory
F. Searle 1-240
2240 Campus Drive
Evanston IL 60208
lab: 847.491.2438
cel: 773.608.9185
email: j-kell...@northwestern.edu
*******************************************
Lijun Liu
Cardiovascular Research Institute
University of California, San Francisco
1700 4th Street, Box 2532
San Francisco, CA 94158
Phone: (415)514-2836
Lijun Liu
Cardiovascular Research Institute
University of California, San Francisco
1700 4th Street, Box 2532
San Francisco, CA 94158
Phone: (415)514-2836
